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Prebiotics and Probiotics for Kids with SIBO

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Small intestinal bacterial overgrowth (SIBO) is on the rise in children, and if left untreated, may cause serious health problems. While the conventional view of SIBO has been that prebiotics and probiotics should be avoided, recent studies suggest that not only are prebiotics and probiotics not harmful for people with SIBO, but they may actually be helpful. Read on to learn about why you should consider incorporating prebiotics and probiotics into treatment protocols for your pediatric SIBO patients.

The Conventional View of SIBO

Small intestinal bacterial overgrowth (SIBO) is a functional gastrointestinal disorder in which excessive bacteria are present in the small intestine. (1) For many years, the conventional view in the SIBO world has been that prebiotics and probiotics should be avoided, including fermented foods and fermentable fibers; this is based on the rationale that since SIBO involves an overgrowth of bacteria in the small intestine, consuming live bacteria (probiotics) or substances that feed bacteria already in the gut (prebiotics) would be harmful.

However, this hesitation has been based on the empirical experience of clinicians testing for and treating SIBO. Recently, studies have emerged suggesting that not only are probiotics and prebiotics not harmful in people with SIBO, they may even be helpful. (2)

Prebiotics and Probiotics May Be Helpful for SIBO

Contrary to conventional recommendations, a growing body of evidence indicates that a combination of prebiotics and probiotics may be beneficial for people with SIBO.

Research demonstrates that prebiotics and probiotics crowd out pathogenic bacteria in the gut, produce natural antibacterial substances, inhibit bacterial translocation, strengthen the immune system, reduce inflammation, and increase gut motility.

These mechanisms help explain the new evidence suggesting that prebiotics and probiotics reduce symptoms of SIBO. (3) A study of probiotic treatment specific for SIBO found that administration of the probiotic Bacillus clausii was comparable to antibiotics for normalizing hydrogen breath tests. (4) In another small study, Lactobacillus casei and Lactobacillus acidophilus were found to be effective for treating diarrhea caused by bacterial overgrowth. (5) A small pilot study found that a probiotic containing Lactobacillus casei, Lactobacillus plantarum, Streptococcus faecalis, and Bifidobacterium brevis was more effective at reducing abdominal distension in SIBO patients compared to the antibiotic metronidazole. (6)

Another pilot study found that a 15-day course of the prebiotic FOS and Bacillus coagulans produced significant improvements in SIBO symptoms after an initial three-week course of broad-spectrum antibiotics. (7) In another study that combined antibiotics with prebiotics and probiotics, it was discovered that administration of rifaximin for seven days, followed by either seven days of Lactobacillus casei or FOS, led to a significant improvement in SIBO symptoms. (8)

Therefore, while the evidence is not conclusive, it appears that prebiotic and probiotic treatment for SIBO may be most effective when used after an initial course of antibiotics. While studies on prebiotic and probiotic treatment for SIBO are limited, the available evidence is encouraging and provides substantial grounds for further research.

SIBO in Children

The prevalence of SIBO in children is higher than previously believed. (9) SIBO may have especially harmful consequences for children due to the malabsorptive state it causes in the small intestine, which can lead to deficiencies in vitamins, minerals, and macronutrients that are crucial for physical growth and development.

Prebiotics and probiotics are helpful, not harmful, for treating SIBO. #probiotics #guthealth

Prebiotics and probiotics may be especially useful treatment options for children with SIBO, as they do not carry the risk of causing diarrhea, C. difficile, allergic reactions, and antibiotic resistance. Before examining the emerging research on prebiotic and probiotic treatment for SIBO in kids, let’s cover some basic information about the potential causes of SIBO in children and the health consequences of untreated SIBO.

What Causes SIBO in Children?

A variety of factors may cause children to develop SIBO. Certain pre-existing health conditions, early childhood risk factors, and the use of certain pharmaceutical drugs may predispose children to SIBO. The common denominator among these factors is that they disrupt mechanisms that normally inhibit bacterial overgrowth in the small intestine.

Pre-Existing Health Conditions

Several pre-existing health conditions may predispose children to SIBO. (10) Abnormalities in the structure of the GI tract, motility disorders, depressed thyroid function, and mitochondrial disorders decrease small intestine motility, causing food and ingested bacteria to stagnate, which may promote bacterial overgrowth. (11, 12) Lowered immunity may also predispose children to SIBO by disrupting normal immune mechanisms in the intestine that keep bacterial counts in check. (13)

Early Childhood Risk Factors

Development of the intestinal microbiome begins in infancy and involves an exchange of microbes between mother and child. Practices that affect this exchange, such as the use of antibiotics during pregnancy, birth by C-section, perinatal antibiotics, and formula feeding, alter the infant microbiome and may predispose a child to dysbiosis and SIBO down the road. (14, 15, 16, 17)

Pharmaceutical Drug Use

Pharmaceutical drugs, including antibiotics, proton pump inhibitors, and H2 receptor blockers, are linked to the development of SIBO in children. Antibiotic use wipes out beneficial gut microbes, increasing the risk of intestinal dysbiosis. (18) Proton pump inhibitors (PPIs) and H2 receptor blockers increase the risk of SIBO by decreasing gastric acid secretion, which is needed to suppress the growth of ingested bacteria. Infants and children are increasingly being prescribed PPIs for GERD, reflux, and colic, and there is a strong association between the use of these drugs and the development of SIBO in children. (19, 20, 21) Concerningly, research indicates that children are at risk of SIBO even after very short-term PPI treatment. (22, 23, 24, 25)

Long-Term Consequences of SIBO in Children

SIBO may have serious health consequences in children. SIBO impairs the intestinal absorption of fats, proteins, carbohydrates, and fat-soluble vitamins, thus depriving a child of these nutrients at a time during which optimal nutrition is crucial for promoting growth and development. (26) SIBO also increases intestinal permeability, a condition that has been linked to systemic inflammation, malnutrition, and growth stunting in children. (27) In addition, untreated SIBO may cause weight loss, retarded growth, iron deficiency anemia, vitamin D deficiency, vitamin B12 deficiency, hypocalcemia, and in severe cases, osteoporosis. (28) It is crucial that children with SIBO be treated promptly to prevent these serious complications.

Prebiotic and Probiotic Treatment May Be Ideal for Kids with SIBO

In adults, the mainstay treatment for SIBO is antibiotic therapy. However, research supporting the use of antibiotics for pediatric patients with SIBO is severely lacking. (29) There are legitimate concerns about the use of antibiotics in children, especially on a recurring basis, as may be required with SIBO treatment. Antibiotics have many side effects, including diarrhea, Clostridium difficile infection, toxic and allergic reactions, and disruption of the gut microbiota.

Considering the lack of evidence supporting antibiotic treatment for children with SIBO, novel treatment options are needed.

Fortunately, emerging research suggests that probiotics and prebiotics may be an ideal alternative to antibiotics for children with SIBO, producing improvements in symptoms without adverse side effects. 

While evidence supporting the potential of prebiotics and probiotics in adults has been accumulating for several years, up until recently, there were no studies examining the efficacy of prebiotics and probiotics for SIBO specifically in children.

However, a recent study found that administration of a synbiotic (a product containing both a prebiotic and a probiotic) produced significant improvement of SIBO symptoms in children, including postprandial abdominal swelling, distension, mucus in stool, constipation, and diarrhea, without any adverse effects. (30) The synbiotic contained Bifidobacterium lactis and inulin.

This study, combined with the studies on adults with SIBO mentioned previously, further supports the idea that prebiotics and probiotics should be embraced, rather than avoided, in the treatment of SIBO.

Conflicting Evidence Regarding FODMAPs and SIBO

This new research supporting prebiotic and probiotic therapy for SIBO raises some important questions. There is good evidence indicating that a low-FODMAP diet is useful for reducing SIBO symptoms such as bloating, diarrhea, and constipation; (31, 32) however, this directly contradicts the evidence laid out here supporting the use of prebiotics (a type of fermentable fiber) for SIBO treatment.

In another apparent contradiction, SIBO patients are often told to avoid fermented foods, yet the research indicates that probiotics help decrease SIBO symptoms. Could these contradictions have to do with individual differences in tolerance of FODMAPs and fermented foods? Could it be that people who have already undergone antimicrobial treatment respond better to prebiotics and probiotics? Could prebiotics and probiotics still be helpful for kids who have not undergone antimicrobial treatment?

Until more conclusive evidence is available to help us answer these questions, dietary experimentation may be necessary in order to determine an individual’s tolerance for fermented foods and FODMAPs while undergoing SIBO treatment.

Vagus Nerve Stimulation May Prevent SIBO Recurrence

A final therapy that is worth mentioning and may nicely complement prebiotic and probiotic therapy for SIBO is vagus nerve stimulation (VNS). Research indicates that low vagal nerve tone alters the migrating motor complex in the gut, reducing gastrointestinal motility and thus allowing bacteria to flourish in the small intestine. VNS has been found to increase gastrointestinal motility and gastric acid production, both of which are important factors for preventing SIBO. (33, 34)

While VNS was originally only available via invasive devices implanted under the skin, there are a couple of non-invasive vagus nerve-stimulating devices available to consumers. These include Nervana (no affiliation), a device that combines vagus nerve stimulation with relaxing music, and pulsed electromagnetic field (PEMF) therapy, which is offered in the form of a handheld device through MicroPulse (no affiliation).

However, these devices are expensive, and may not be the best choice for everyone. For those looking for a more cost-conscious option, acupuncture and massage may be  good choices, since both of these modalities stimulate the vagus nerve.

Finally, the practice of certain exercises, such as gargling and stimulating the soft palate with a tongue depressor, have been found to stimulate the vagus nerve. Patients may want to consider working under the supervision of a healthcare practitioner trained in vagus nerve stimulation, such as a functional neurologist, who can provide vagus nerve stimulation using devices that are not available direct to consumer.

Whichever route a patient chooses to take, restoration of GI motility and gastric acid production through VNS  may nicely complement prebiotic and probiotic SIBO treatment in children.


  1. As always Chris, great article. My daughter suffered from SIBO symptoms for several years after a bad stomach flu. Desperate and wanting to avoid antibiotics for her i secured some Bacillus Clausii from Italy. Two full one month rounds of this done at two separate intertervals and she rarely ever complains and now eats a normal diet including having pizza or treats when she is at birthday parties, etc. I now am giving her megasporebiotic several times a week as maintenance since it contains the same strain. But the Bacillus Clausii was truly miraculous. I guess i we did a bit of prebiotic therapy by accident in that she basically resumed a low sugar but normal American diet after the probiotic therapy. I will look into the other suggestions as I had avoided inulin (I do think she has had some in Kind Bars, etc) Thanks Chris!!!

    • GREAT article Chris, thank you!!! I have recently been diagnosed with SIBO & worry that my son is afflicted with it. He is 4 & has battled horrible constipation his whole life. I wanted to go the natural route and cut out dairy & gave him a complete probiotic & magnesium powder. It seems to have really helped but he still doesn’t go to bathroom every day.

      Mimi…where can I get the probiotic you gave you daughter?? The bacillus Clausii and the megasporbiotic? And how long was “the 2 rounds”? I don’t want him to be afflicted with this for the rest of his life!
      Thank you,

    • Can you please tell us the brand you got from Italy with the web sight you ordered from. Thank you

    • Can you please let me know what brands you used? I really need to find something to help my 10yr old. I think Sibo is the cause of her nausea and therefore her chronic anxiety. Your help would be much appreciated! 🙂

      • Hi, I have a 9 year old that has battled terrible nausea for 10 months now. The drs have tried all the normal steps and tests and just got his endoscopy results and they say he has ileitis. He losing weight. He also has anxiety that is getting worse. Please let me know if you have found any resources.

        • Hi Rebecca,

          I have an 11 year old son who has had chronic nausea for the past 12 months. We’ve been through the medical system with no relief. We only saw some results when we started working with a Naturopath and now a Functional Medicine practitioner. Through a Comprehensive Stool Analysis, a SIBO test and allergy testing we’ve found that he has Candida, SIBO and food allergies. He had some relief from the nausea after being on Nystatin (anti fungal) for a couple of months but is really sick again now that I’ve removed foods which can be contributing to SIBO (due to die off). I meet with the dr this week so will know more then. Hopefully, this may help. Good luck

  2. Great blog post, thank you for the update on these multi-disciplinary approaches to SIBO. One question: do you have specific prebiotic and probiotic type and strain recommendations for kids and young adults who show high D-lactate?

  3. You forgot to mention acellular carbs, i.e. refined stuff. Acellular carbs promote bacterial overgrowth in the small intestine.
    The fact that vagal stimulation helps reinforces Spreadbury’s theory that says that acellular carbs provoke dysbiosis in the small intestine with the consequence vagal afferent inflammation. Since the body usually works bidirectionally, there’s no wonder if it works in all the other way around as well.

  4. Vagal Tone from Meo Energetics looks very promising. Would love for you to check it out and review it.

  5. Chris what’s your opinion on probiotics with bacteriophage in them? Any research showing phages benefit SIBO

  6. Thanks for sharing Chris.

    I usually would give probiotics to my paediatric patients who had just undergone antibiotics treatment, as they always complaint of diarrhoea post antibiotics. That would be a 1 – 2 weeks course of probiotics, then I’d make sure they take their daily prebiotic supplement.

    Is it ok if I translate your article into my native language to spread awareness, and credit back to you?

    – Aimi

    • Hi Aimi,

      Thanks for asking. Because we sometimes make updates to blog articles, we’d prefer if you link people directly to the article. Many browsers—such as Chrome—have a built-in translation feature.

  7. Excellent article Chris. Concerning the “conflicting evidence regarding FODMAPs and SIBO”, one possible explanation is the amount of prebiotic used. I haven’t checked each referenced study, but typical amounts of prebiotic given with probiotics are in the gram/sub-gram range. That’s not a significant amount of fermentable material – perhaps just enough to help some strains get going. But diets higher in FODMAPs and other fermentable carbs can easily include well over 100 grams if you add fiber, resistant starch and other FODMAPs. The study by Piche,, is a good example of what happens when you add higher amounts of prebiotic. In this case, they gave fructose oligosaccharide (6.6 grams 3x/day) to people with GERD – arguably SIBO-related. They found that “Compared with placebo, FOS led to a significant increase in the number of transient lower esophageal sphincter relaxations (TLESRs) and reflux episodes, esophageal acid exposure, and the symptom score for GERD”.

  8. Thanks for the great article, Chris!

    I suspect my 2-year-old has SIBO. Traditional doctors have tested him for many things, and everything is coming back negative. I have done some controlled FODMAP testing, and, once given a high FODMAP food, he reacts.

    Do you know if/how I can get him an official SIBO test to know for sure?

  9. Is organix dysbiosis urine test an accurate enough test for detecting SIBO for my 4 year old? The diet and length of the breath test looks very daunting.